Pine City is located at 45°49'32" North, 92°58'5" West (45.825833, -92.968056).

According to the United States Census Bureau, the city has a total area of 3.23 mi2 (8.37 km2). 2.83 mi2 (7.32 km2) of it is land and 0.41 mi2 (1.05 km2) of it is covered by water. The total area is 12.56% water.

Pine City is located in the Central Standard Time (CST) timezone, GMT-06:00. It observes Daylight Saving Time (DST).